diff dynamic_tool_wrappers_macros.xml @ 0:b49e227ec738 draft default tip

planemo upload commit fe1408d418f7f1354a736f73ece704219baa3190

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dynamic_tool_wrappers_macros.xml	Wed Mar 21 17:26:27 2018 -0400
@@ -0,0 +1,189 @@
+<macros>
+
+    <xml name="rmarkdown_requirements">
+        <requirement type="package" version="1.15.0.6-0">pandoc</requirement>
+        <requirement type="package" version="1.20.0">r-getopt</requirement>
+        <requirement type="package" version="1.6">r-rmarkdown</requirement>
+    </xml>
+
+    <xml name="stdio">
+        <stdio>
+            <regex match="XXX" source="stderr" level="warning"
+                   description="Check the tool log output file for more details."/>
+        </stdio>
+    </xml>
+
+    <!--Tool name-->
+    <xml name="tool_name">
+        <param type="select" name="tool_name" multiple="false" label="Tool name">
+            <option value="fastqc" selected="false">fastqc</option>
+        </param>
+    </xml>
+
+    <!--OPTION/ARGUMENT PAIRS and INPUT types-->
+    <!--input files-->
+    <xml name="option_argument_one_dataset">
+        <repeat name="option_argument_one_dataset_repeat" title="OPTION and ARGUMENT: input one dataset" min="0" default="0">
+            <param type="text" name="flag" optional="true" label="flag" />
+            <param name="one_dataset" type="data" optional="true" multiple="false" label="value"/>
+        </repeat>
+    </xml>
+    <xml name="option_argument_multiple_datasets">
+        <repeat name="option_argument_multiple_datasets_repeat" title="OPTION and ARGUMENT: input multiple datasets" min="0" default="0">
+            <param type="text" name="flag" optional="true" label="flag" />
+            <param name="multiple_datasets" type="data" optional="true" multiple="true" label="value" />
+        </repeat>
+    </xml>
+    <xml name="option_argument_path_relative_to_upstream_tool">
+        <repeat name="option_argument_path_relative_to_upstream_tool_repeat" title="OPTION and ARGUMENT: path relative to upstream tool" min="0" default="0">
+            <param type="text" name="flag" optional="true" label="flag" />
+            <param name="upstream_tool_output_dir" type="data" optional="true" multiple="false" label="upstream tool output directory"/>
+            <param type="text" name="option_argument_path" optional="true" label="value" />
+        </repeat>
+    </xml>
+
+    <!--input values: string, float and integer-->
+    <xml name="option_argument_string">
+        <repeat name="option_argument_string_repeat" title="OPTION and ARGUMENT: input string" min="0" default="0">
+            <param type="text" name="flag" label="flag" />
+            <param type="text" name="option_argument_string"  label="value" />
+        </repeat>
+    </xml>
+    <xml name="option_argument_float">
+        <repeat name="option_argument_float_repeat" title="OPTION and ARGUMENT: input float" min="0" default="0">
+            <param type="text" name="flag" label="flag" />
+            <param type="text" name="option_argument_float"  label="value" />
+        </repeat>
+    </xml>
+    <xml name="option_argument_integer">
+        <repeat name="option_argument_integer_repeat" title="OPTION and ARGUMENT: input integer" min="0" default="0">
+            <param type="text" name="flag" label="flag" />
+            <param type="text" name="option_argument_integer"  label="value" />
+        </repeat>
+    </xml>
+
+    <!--output set-->
+    <xml name="output_set">
+        <data format="html" name="report" label="${tool.name} report"/>
+        <data format="txt" name="tool_help_doc" label="${tool.name} help doc"/>
+        <data format="txt" name="tool_output_dir" label="${tool.name} output directory"/>
+        <data format="txt" name="tool_log" label="${tool.name} log" from_work_dir="tool_log.txt"/>
+    </xml>
+
+
+    <!--shell command fragment-->
+    <xml name="shell_command">
+        <command><![CDATA[
+        export TOOL_DIR='${__tool_directory__}' &&
+
+        Rscript '${__tool_directory__}/dynamic_tool_render.R'
+
+        ############ tool_name
+        -t '$tool_name'
+
+        ############ option_argument_one_dataset
+        #set sep = ''
+        #set one_dataset_items = ''
+        #for i in $option_argument_one_dataset_repeat:
+            #set one_dataset_items += $sep + $option_argument_one_dataset_repeat.flag + " " + $option_argument_one_dataset_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -o '$one_dataset_items'
+
+
+
+        ############ option_argument_multiple_datasets
+        #set sep = ''
+        #set multiple_datasets_items = ''
+        #for i in $option_argument_multiple_datasets_repeat:
+            #set multiple_datasets_items += $sep + $option_argument_multiple_datasets_repeat.flag + " " + $option_argument_multiple_datasets_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -m '$multiple_datasets_items'
+
+
+        ############ option_argument_path_relative_to_upstream_tool
+        #set sep = ''
+        #set path_relative_to_upstream_tool_items = ''
+        #for i in $option_argument_path_relative_to_upstream_tool_repeat:
+            #set path_relative_to_upstream_tool_items += $sep + $option_argument_path_relative_to_upstream_tool_repeat.flag + " " + $option_argument_path_relative_to_upstream_tool_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -u '$path_relative_to_upstream_tool_items'
+        
+        
+
+        ############ option_argument_string
+        #set sep = ''
+        #set string_items = ''
+        #for i in $option_argument_string_repeat:
+            #set string_items += $sep + $option_argument_string_repeat.flag + " " + $option_argument_string_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -s '$string_items'
+        
+
+        ############ option_argument_float
+        #set sep = ''
+        #set float_items = ''
+        #for i in $option_argument_float_repeat:
+            #set float_items += $sep + $option_argument_float_repeat.flag + " " + $option_argument_float_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -f '$float_items'
+
+        ############ option_argument_integer
+        #set sep = ''
+        #set integer_items = ''
+        #for i in $option_argument_integer_repeat:
+            #set integer_items += $sep + $option_argument_integer_repeat.flag + " " + $option_argument_integer_repeat.value + "'"
+            #### separate values set by repeat
+            $set sep = '|'
+        #end for
+
+        -i '$integer_items'
+
+
+        ############ output_set
+        -R '$report'
+        -D '$report.files_path'
+        -H '$tool_help_doc'
+        -O '$tool_output_dir'
+        -L '$tool_log'
+
+        ]]></command>
+    </xml>
+
+    <!--tool citations-->
+    <xml name="citations">
+        <citation type="bibtex"><![CDATA[
+            @article{allaire2016rmarkdown,
+            title={rmarkdown: Dynamic Documents for R, 2016},
+            author={Allaire, J and Cheng, Joe and Xie, Yihui and McPherson, Jonathan and Chang, Winston and Allen, Jeff
+            and Wickham, Hadley and Atkins, Aron and Hyndman, Rob},
+            journal={R package version 0.9},
+            volume={6},
+            year={2016}
+            }
+        ]]></citation>
+        <citation type="bibtex"><![CDATA[
+            @book{xie2015dynamic,
+            title={Dynamic Documents with R and knitr},
+            author={Xie, Yihui},
+            volume={29},
+            year={2015},
+            publisher={CRC Press}
+            }
+        ]]></citation>
+    </xml>
+</macros>
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